HEADER TRANSFERASE 06-JUN-03 1PKV TITLE THE N-TERMINAL DOMAIN OF RIBOFLAVIN SYNTHASE IN COMPLEX WITH TITLE 2 RIBOFLAVIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOFLAVIN SYNTHASE ALPHA CHAIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN; COMPND 5 EC: 2.5.1.9; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: RIBE OR RIBC OR B1662 OR SF1690; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_CELL_LINE: XL1-BLUE CELLS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PNCO113 KEYWDS DIMER, BETA-BARREL, GREEK KEY MOTIF, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR W.MEINING,S.EBERHARDT,A.BACHER,R.LADENSTEIN REVDAT 4 16-AUG-23 1PKV 1 REMARK REVDAT 3 13-JUL-11 1PKV 1 VERSN REVDAT 2 24-FEB-09 1PKV 1 VERSN REVDAT 1 08-JUN-04 1PKV 0 JRNL AUTH W.MEINING,S.EBERHARDT,A.BACHER,R.LADENSTEIN JRNL TITL THE STRUCTURE OF THE N-TERMINAL DOMAIN OF RIBOFLAVIN JRNL TITL 2 SYNTHASE IN COMPLEX WITH RIBOFLAVIN AT 2.6A RESOLUTION. JRNL REF J.MOL.BIOL. V. 331 1053 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12927541 JRNL DOI 10.1016/S0022-2836(03)00844-1 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.EBERHARDT,N.ZINGLER,K.KEMTER,G.RICHTER,M.CUSHMAN,A.BACHER REMARK 1 TITL DOMAIN STRUCTURE OF RIBOFLAVIN SYNTHASE REMARK 1 REF EUR.J.BIOCHEM. V. 268 4315 2001 REMARK 1 REFN ISSN 0014-2956 REMARK 1 DOI 10.1046/J.1432-1327.2001.02351.X REMARK 1 REFERENCE 2 REMARK 1 AUTH B.ILLARIONOV,K.KEMTER,S.EBERHARDT,G.RICHTER,M.CUSHMAN, REMARK 1 AUTH 2 A.BACHER REMARK 1 TITL RIBOFLAVIN SYNTHASE OF ESCHERICHIA COLI. EFFECT OF SINGLE REMARK 1 TITL 2 AMINO ACID SUBSTITUTIONS ON REACTION RATE AND LIGAND BINDING REMARK 1 TITL 3 PROPERTIES REMARK 1 REF J.BIOL.CHEM. V. 276 11524 2001 REMARK 1 REFN ISSN 0021-9258 REMARK 1 DOI 10.1074/JBC.M008931200 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 6793 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 337 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 475 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE SET COUNT : 31 REMARK 3 BIN FREE R VALUE : 0.3180 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1330 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 37 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.58000 REMARK 3 B22 (A**2) : 2.17000 REMARK 3 B33 (A**2) : -0.59000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.485 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.281 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.188 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.765 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.906 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1372 ; 0.020 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1869 ; 1.798 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 170 ; 6.087 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 225 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 997 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 544 ; 0.219 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 65 ; 0.183 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 44 ; 0.318 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 848 ; 1.068 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1373 ; 2.151 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 524 ; 3.216 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 496 ; 5.286 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 3 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 18 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 2 A 15 1 REMARK 3 1 B 2 B 15 1 REMARK 3 2 A 16 A 17 3 REMARK 3 2 B 16 B 17 3 REMARK 3 3 A 21 A 21 1 REMARK 3 3 B 21 B 21 1 REMARK 3 4 A 22 A 22 3 REMARK 3 4 B 22 B 22 3 REMARK 3 5 A 23 A 32 1 REMARK 3 5 B 23 B 32 1 REMARK 3 6 A 67 A 68 1 REMARK 3 6 B 67 B 68 1 REMARK 3 7 A 70 A 76 1 REMARK 3 7 B 70 B 76 1 REMARK 3 8 A 18 A 20 6 REMARK 3 8 B 18 B 20 6 REMARK 3 9 A 64 A 66 5 REMARK 3 9 B 64 B 66 5 REMARK 3 10 A 55 A 57 3 REMARK 3 10 B 55 B 57 3 REMARK 3 11 A 58 A 63 1 REMARK 3 11 B 58 B 63 1 REMARK 3 12 A 69 A 69 5 REMARK 3 12 B 69 B 69 5 REMARK 3 13 A 33 A 34 3 REMARK 3 13 B 33 B 34 3 REMARK 3 14 A 35 A 36 1 REMARK 3 14 B 35 B 36 1 REMARK 3 15 A 37 A 37 3 REMARK 3 15 B 37 B 37 3 REMARK 3 16 A 38 A 54 1 REMARK 3 16 B 38 B 54 1 REMARK 3 17 A 77 A 77 3 REMARK 3 17 B 77 B 77 3 REMARK 3 18 A 78 A 87 1 REMARK 3 18 B 78 B 87 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 551 ; 0.08 ; 0.05 REMARK 3 MEDIUM POSITIONAL 1 A (A): 16 ; 0.21 ; 0.50 REMARK 3 LOOSE POSITIONAL 1 A (A): 63 ; 0.89 ; 5.00 REMARK 3 TIGHT THERMAL 1 A (A**2): 551 ; 0.22 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 16 ; 0.98 ; 2.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 63 ; 4.04 ; 10.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 100 A 100 1 REMARK 3 1 B 101 B 101 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 2 B (A): 27 ; 0.04 ; 0.05 REMARK 3 TIGHT THERMAL 2 B (A**2): 27 ; 0.31 ; 0.50 REMARK 3 REMARK 3 NCS GROUP NUMBER : 3 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 101 A 116 1 REMARK 3 1 B 103 B 116 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 3 A (A): 7 ; 0.13 ; 0.05 REMARK 3 TIGHT THERMAL 3 A (A**2): 7 ; 0.55 ; 0.50 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 CHAINS C AND D IN NCS GROUP 2 CORRESPOND TO THE RESIDUES REMARK 3 100 AND 101 IN THE COORDINATES; CHAIN E IN NCS GROUP 3 REMARK 3 CORRESPONDS TO WATER MOLECULES 1-17, 32, 34, 36, 37 REMARK 3 AND CHAIN F IN NCS GROUP 3 CORRESPONDS TO WATER MOLECULES REMARK 3 18-31, 33, 35 IN THE COORDINATES REMARK 4 REMARK 4 1PKV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUN-03. REMARK 100 THE DEPOSITION ID IS D_1000019397. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-00 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8424 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7131 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1I8D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 70 MM SODIUM POTASSIUM PHOSPHATE, PH REMARK 280 7.0, 100 MM SODIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.55650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.55650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 25.08050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.19150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 25.08050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.19150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 42.55650 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 25.08050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 52.19150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 42.55650 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 25.08050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 52.19150 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE ASYMMETRIC UNIT CONTAINS THE DIMER, WHICH IS ALSO FOUND REMARK 300 IN SOLUTION REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A 88 REMARK 465 LYS A 89 REMARK 465 PHE A 90 REMARK 465 SER A 91 REMARK 465 ASP A 92 REMARK 465 GLU A 93 REMARK 465 ILE A 94 REMARK 465 GLY A 95 REMARK 465 GLY A 96 REMARK 465 HIS A 97 REMARK 465 ALA B 88 REMARK 465 LYS B 89 REMARK 465 PHE B 90 REMARK 465 SER B 91 REMARK 465 ASP B 92 REMARK 465 GLU B 93 REMARK 465 ILE B 94 REMARK 465 GLY B 95 REMARK 465 GLY B 96 REMARK 465 HIS B 97 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 ASN B 20 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 MET A 1 CE REMARK 480 LYS A 11 CE NZ REMARK 480 GLU A 37 OE1 OE2 REMARK 480 ASN A 55 OD1 ND2 REMARK 480 LYS A 65 CD CE NZ REMARK 480 GLU A 66 OE1 OE2 REMARK 480 ARG A 69 CZ NH1 NH2 REMARK 480 LYS A 77 CE NZ REMARK 480 ASP B 34 OD1 OD2 REMARK 480 GLU B 37 OE1 OE2 REMARK 480 LYS B 65 CE NZ REMARK 480 LYS B 77 CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 C PRO B 19 CA ASN B 20 1.63 REMARK 500 O PRO B 19 CA ASN B 20 1.80 REMARK 500 OE2 GLU B 66 NH1 ARG B 69 2.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 11 CD LYS A 11 CE -0.514 REMARK 500 GLU A 37 CD GLU A 37 OE1 0.105 REMARK 500 GLU A 37 CD GLU A 37 OE2 -0.104 REMARK 500 ARG A 69 NE ARG A 69 CZ -0.262 REMARK 500 LYS A 77 CD LYS A 77 CE 0.262 REMARK 500 PRO B 19 C ASN B 20 N -0.399 REMARK 500 ASP B 34 CG ASP B 34 OD1 -0.154 REMARK 500 ASP B 34 CG ASP B 34 OD2 0.168 REMARK 500 GLU B 37 CD GLU B 37 OE1 -0.158 REMARK 500 GLU B 37 CD GLU B 37 OE2 0.125 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS A 11 CD - CE - NZ ANGL. DEV. = 35.6 DEGREES REMARK 500 GLU A 37 CG - CD - OE1 ANGL. DEV. = 12.4 DEGREES REMARK 500 ASP A 62 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG A 69 CD - NE - CZ ANGL. DEV. = 16.2 DEGREES REMARK 500 ARG A 69 NE - CZ - NH1 ANGL. DEV. = -12.6 DEGREES REMARK 500 ARG A 69 NE - CZ - NH2 ANGL. DEV. = 12.1 DEGREES REMARK 500 PRO B 19 CA - C - N ANGL. DEV. = -13.7 DEGREES REMARK 500 ASN B 20 C - N - CA ANGL. DEV. = -37.1 DEGREES REMARK 500 ASN B 20 CA - C - N ANGL. DEV. = -23.1 DEGREES REMARK 500 ASN B 20 O - C - N ANGL. DEV. = 17.2 DEGREES REMARK 500 PHE B 21 C - N - CA ANGL. DEV. = -17.2 DEGREES REMARK 500 ASP B 34 CB - CG - OD1 ANGL. DEV. = 10.8 DEGREES REMARK 500 ASP B 34 CB - CG - OD2 ANGL. DEV. = -8.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 14 136.77 -173.04 REMARK 500 LYS B 18 -159.43 -129.73 REMARK 500 ASN B 20 -20.20 -150.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLU B 37 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 PRO B 19 -16.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RBF A 100 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RBF B 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HZE RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF RIBOFLAVIN SYNTHASE REMARK 900 FROM E. COLI REMARK 900 RELATED ID: 1I8D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RIBOFLAVIN SYNTHASE REMARK 900 RELATED ID: 1KZL RELATED DB: PDB REMARK 900 RIBOFLAVIN SYNTHASE FROM S. POMBE BOUND TO CARBOXYETHYLLUMAZINE DBREF 1PKV A 1 97 UNP P29015 RISA_ECOLI 1 97 DBREF 1PKV B 1 97 UNP P29015 RISA_ECOLI 1 97 SEQRES 1 A 97 MET PHE THR GLY ILE VAL GLN GLY THR ALA LYS LEU VAL SEQRES 2 A 97 SER ILE ASP GLU LYS PRO ASN PHE ARG THR HIS VAL VAL SEQRES 3 A 97 GLU LEU PRO ASP HIS MET LEU ASP GLY LEU GLU THR GLY SEQRES 4 A 97 ALA SER VAL ALA HIS ASN GLY CYS CYS LEU THR VAL THR SEQRES 5 A 97 GLU ILE ASN GLY ASN HIS VAL SER PHE ASP LEU MET LYS SEQRES 6 A 97 GLU THR LEU ARG ILE THR ASN LEU GLY ASP LEU LYS VAL SEQRES 7 A 97 GLY ASP TRP VAL ASN VAL GLU ARG ALA ALA LYS PHE SER SEQRES 8 A 97 ASP GLU ILE GLY GLY HIS SEQRES 1 B 97 MET PHE THR GLY ILE VAL GLN GLY THR ALA LYS LEU VAL SEQRES 2 B 97 SER ILE ASP GLU LYS PRO ASN PHE ARG THR HIS VAL VAL SEQRES 3 B 97 GLU LEU PRO ASP HIS MET LEU ASP GLY LEU GLU THR GLY SEQRES 4 B 97 ALA SER VAL ALA HIS ASN GLY CYS CYS LEU THR VAL THR SEQRES 5 B 97 GLU ILE ASN GLY ASN HIS VAL SER PHE ASP LEU MET LYS SEQRES 6 B 97 GLU THR LEU ARG ILE THR ASN LEU GLY ASP LEU LYS VAL SEQRES 7 B 97 GLY ASP TRP VAL ASN VAL GLU ARG ALA ALA LYS PHE SER SEQRES 8 B 97 ASP GLU ILE GLY GLY HIS HET RBF A 100 27 HET RBF B 101 27 HETNAM RBF RIBOFLAVIN HETSYN RBF RIBOFLAVINE; VITAMIN B2 FORMUL 3 RBF 2(C17 H20 N4 O6) FORMUL 5 HOH *37(H2 O) HELIX 1 1 PRO A 29 LEU A 33 5 5 HELIX 2 2 LYS A 65 THR A 71 1 7 HELIX 3 3 ASN A 72 LEU A 76 5 5 HELIX 4 4 PRO B 29 LEU B 33 5 5 HELIX 5 5 MET B 64 THR B 71 1 8 HELIX 6 6 ASN B 72 LEU B 76 5 5 SHEET 1 A 7 GLY A 8 GLU A 17 0 SHEET 2 A 7 PHE A 21 GLU A 27 -1 O VAL A 25 N SER A 14 SHEET 3 A 7 HIS A 58 MET A 64 -1 O LEU A 63 N ARG A 22 SHEET 4 A 7 CYS A 47 ASN A 55 -1 N GLU A 53 O SER A 60 SHEET 5 A 7 SER A 41 HIS A 44 -1 N HIS A 44 O CYS A 47 SHEET 6 A 7 TRP A 81 ARG A 86 -1 O GLU A 85 N ALA A 43 SHEET 7 A 7 GLY A 8 GLU A 17 -1 N ALA A 10 O VAL A 82 SHEET 1 B 7 GLY B 8 GLU B 17 0 SHEET 2 B 7 ARG B 22 GLU B 27 -1 O VAL B 25 N SER B 14 SHEET 3 B 7 HIS B 58 LEU B 63 -1 O LEU B 63 N ARG B 22 SHEET 4 B 7 CYS B 47 ASN B 55 -1 N GLU B 53 O SER B 60 SHEET 5 B 7 SER B 41 HIS B 44 -1 N HIS B 44 O CYS B 47 SHEET 6 B 7 TRP B 81 ARG B 86 -1 O GLU B 85 N ALA B 43 SHEET 7 B 7 GLY B 8 GLU B 17 -1 N GLY B 8 O VAL B 84 SITE 1 AC1 16 CYS A 47 CYS A 48 LEU A 49 THR A 50 SITE 2 AC1 16 ASP A 62 LEU A 63 MET A 64 THR A 67 SITE 3 AC1 16 HOH A 101 HOH A 114 GLY B 4 ILE B 5 SITE 4 AC1 16 VAL B 6 MET B 64 GLU B 66 RBF B 101 SITE 1 AC2 18 GLY A 4 ILE A 5 VAL A 6 THR A 50 SITE 2 AC2 18 ASP A 62 MET A 64 RBF A 100 CYS B 47 SITE 3 AC2 18 CYS B 48 LEU B 49 THR B 50 ASP B 62 SITE 4 AC2 18 LEU B 63 MET B 64 THR B 67 THR B 71 SITE 5 AC2 18 HOH B 102 HOH B 103 CRYST1 50.161 104.383 85.113 90.00 90.00 90.00 C 2 2 21 16 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.019936 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009580 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011749 0.00000